{"database": "metadata", "table": "run_metadata", "rows": [[29111, "SRR27151547", "SRX22833139", "SRS19813579", "SRP476691", "PRJNA1050282", "Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye]", "GSE249751", "Transcriptome Analysis", "The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones\u2014analogous to the transformation of red to red/UV cones that occurs in zebrafish\u2014and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4\u00b0C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/\u00b5l 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.", "parent bioproject:PRJNA1050288", "pubmed:39531499", null, "5 dpf larval eyes  WT  rep2", "GSM7963637", null, "source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing", "5 dpf larval eyes  WT  rep2", "Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf larval eyes. Genes are ranked by p adj.", "eye", null, "To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4\u00b0C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/\u00b5l 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer\u2019s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3\u2019 ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.", null, "tissue:eye|developmental stage:5 dpf larvae|genotype:WT", "GSM7963637", "GSM7963637: 5 dpf larval eyes  WT  rep2; Danio rerio; RNA Seq", "GSM7963637 r1", "GSM7963637", "1", "To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4\u00b0C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/\u00b5l 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP476691", null, "loader:fastq load.py", "w8.AATCTCAGGC-TCACCAGGAC.H37F5DSX2_AATCTCAGGC-TCACCAGGAC_L003_R1.fastq.gz w8.AATCTCAGGC-TCACCAGGAC.H37F5DSX2_AATCTCAGGC-TCACCAGGAC_L003_R2.fastq.gz", "fastq fastq", 10471048190.0, 34672345.0, "GSM7963637 r1", "0:151 1:151", "A:2767212261;C:2402799397;G:2644524852;T:2656347723;N:163957", 151, 151, null, null, 2767212261, 2402799397, 2644524852, 2656347723, 163957, "SRX22833139", "SRS19813579", "SRA1765718", "Pathology and Immunology, Washington University School of Medicine", "Pathology and Immunology, Washington University School of Medicine", 2, 0.95909, 0.96443, 0.04132, 0.04289, 0.74217, 0.74631, 0.40379, 0.41076, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "random_priming", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-12-08", "Larval", "Larval", "Eye", "Sensory System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["29111"], "units": {}, "query_ms": 9.658914001192898}